The isotopic composition of Fe was determined in water, Fe-oxides and sulfides from the Tinto and Odiel Basins (South West Spain). As a consequence of sulfide oxidation in mine tailings both rivers are acidic (1.45 < pH < 3.85) and display high concentrations of dissolved Fe (up to 420 mmol l− 1) and sulphates (up to 1190 mmol l− 1). The δ56Fe of pyrite-rich samples from the Rio Tinto and from the Tharsis mine ranged from − 0.56 ± 0.08‰ to + 0.25 ± 0.1‰. δ56Fe values for Fe-oxides precipitates that currently form in the riverbed varied from − 1.98 ± 0.10‰ to 1.57 ± 0.08‰. Comparatively narrower ranges of values (− 0.18 ± 0.08‰ and + 0.21 ± 0.14‰) were observed in their fossil analogues from the Pliocene-Pleistocene and in samples from the Gossan (the oxidized layer that formed through exposure to oxygen of the massive sulfide deposits) (− 0.36 ± 0.12‰ to 0.82 ± 0.07‰). In water, δ56Fe values ranged from − 1.76 ± 0.10‰ to + 0.43 ± 0.05‰. At the source of the Tinto River, fractionation between aqueous Fe(III) and pyrite from the tailings was less than would be expected from a simple pyrite oxidation process. Similarly, the isotopic composition of Gossan oxides and that of pyrite was different from what would be expected from pyrite oxidation. In rivers, the precipitation of Fe-oxides (mainly jarosite and schwertmannite and lesser amounts of goethite) from water containing mainly (more than 99%) Fe(III) with concentrations up to 372 mmol l− 1 causes variable fractionation between the solid and the aqueous phase (− 0.98‰ < Δ56Fesolid-water < 2.25‰). The significant magnitude of the positive fractionation factor observed in several Fe(III) dominated water may be related to the precipitation of Fe(III) sulphates containing phases.